The result of plink –freq is filled with NA

The result of plink –freq is filled with NA

0

I downloaded the vcf file. Then I used plink to convert it to a bed file and calculated the array frequency.

However, the result of plink –freq was filled with NA.

Can anyone give us an opinion?

command

① ./plink –vcf ebi-a-GCST010775.vcf.gz –keep-allele-order –out covid –maf 0.2 –make-bed

② wc covid.*

0 1 9194292 covid.bed

9194289 55165734 262203653 covid.bim

1 6 43 covid.fam

30 146 1068 covid.log

③  ./plink –bfile covid –out COVID_1 –freq

④ head -n 5 COVID_1.frq

CHR SNP A1 A2 MAF NCHROBS
1 rs61769339 A G NA 0

1 rs12238997 G A NA 0

1 rs61769351 C G NA 0

1 rs144155419 A G NA 0

1 rs12565286 C G NA 0


–freq


vcf


SNP


NP


PLINK

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